[gmx-users] pdb2gmx, charmm22 and HEME

[Justin Lemkul]

On 4/29/14, 5:13 PM, Erik Marklund wrote:
> Dear users,
>
> I am trying to preprocess a cytochrome C structure with pdb2gmx and have run into some problems. The forcefield has parameters for the HEME group, but other components are missing to successfully produce the topology etc. First of all, the hdb files don't have an entry for HEME, but I managed to make one myself (which I am happy to share with the gromacs community). What's worse however, is that the histidine that sits bang on top of the Fe in the HEME is turned into a HIS1, which isn't found in the ftp files:
>
> ...
> Linking CYS-14 SG-109 and HEM-105 CAB-845...
> Linking CYS-17 SG-129 and HEM-105 CAC-853...
> Linking HIS-18 NE2-139 and HEM-105 FE-866...
> Linking MET-80 SD-626 and HEM-105 FE-866...
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.6-dev-20131203-a2e1958-unknown
> Source code file: /u/jlpb/marklund/src/gmx/release-4-6/gromacs/src/kernel/resall.c, line: 642
>
> Fatal error:
> Residue 'HIS1' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> How do I resolve this issue? This has been discussed in the mailing list before, but so far I've only found dead ends
>

The HIS1 nomenclature is tailored to Gromos and OPLS, both of which declare a 
special HIS1 residue in the .rtp that is a clone of HIS-delta (HISA in Gromos). 
  For CHARMM, the equivalent would be to declare HSD as the ligating residue. 
Presumably, replacing HIS1 with HSD in specbond.dat (a local copy should 
override the one in $GMXLIB) will fix this.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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